]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added rename.seqs command.
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 2e61594d5719fa20176872c5c35140882901a649..77cfb8c6cd50b9ec16746ef64d16f142be6fb8dc 100644 (file)
@@ -3,61 +3,83 @@
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+       objectVersion = 46;
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                A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; };
@@ -72,7 +94,6 @@
                A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66412D37EC400DA6239 /* blastdb.cpp */; };
                A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66612D37EC400DA6239 /* boneh.cpp */; };
                A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66812D37EC400DA6239 /* bootstrap.cpp */; };
-               A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */; };
                A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66C12D37EC400DA6239 /* bstick.cpp */; };
                A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66E12D37EC400DA6239 /* calculator.cpp */; };
                A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67012D37EC400DA6239 /* canberra.cpp */; };
                A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */; };
                A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */; };
                A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */; };
-               A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */; };
+               A7E9B8B312D37EC400DA6239 /* consensus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B512D37EC400DA6239 /* consensus.cpp */; };
                A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */; };
                A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */; };
                A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6BB12D37EC400DA6239 /* coverage.cpp */; };
                A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */; };
                A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */; };
                A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */; };
-               A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E512D37EC400DA6239 /* fisher2.c */; };
                A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E712D37EC400DA6239 /* flowdata.cpp */; };
                A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */; };
                A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6EC12D37EC400DA6239 /* formatphylip.cpp */; };
                A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */; };
                A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75112D37EC400DA6239 /* mempearson.cpp */; };
                A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */; };
-               A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75612D37EC400DA6239 /* metastats2.c */; };
                A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */; };
                A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */; };
                A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75B12D37EC400DA6239 /* mothur.cpp */; };
                A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78312D37EC400DA6239 /* parsimony.cpp */; };
                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */; };
                A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */; };
-               A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */; };
                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */; };
                A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */; };
                A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78F12D37EC400DA6239 /* phylotree.cpp */; };
                A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B012D37EC400DA6239 /* readblast.cpp */; };
                A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B212D37EC400DA6239 /* readcluster.cpp */; };
                A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */; };
-               A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */; };
-               A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */; };
                A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */; };
                A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BF12D37EC400DA6239 /* readtree.cpp */; };
-               A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */; };
                A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */; };
                A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */; };
                A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */; };
                A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87C12D37EC400DA6239 /* weighted.cpp */; };
                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; };
                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; };
+               A7EEB0F514F29BFE00344B83 /* classifytreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */; };
                A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */; };
                A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FA10011302E096003860FE /* mantelcommand.cpp */; };
                A7FA2AC714A0E881007C09A6 /* bsplvb.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2ABC14A0E881007C09A6 /* bsplvb.f */; };
                        outputFiles = (
                                "$(TARGET_BUILD_DIR)/$(INPUT_FILE_BASE).o",
                        );
-                       script = "/usr/local/gfortran/bin/gfortran -g -m64 -c ${PROJECT_DIR}/${INPUT_FILE_NAME} -o ${TARGET_BUILD_DIR}/${INPUT_FILE_BASE}.o";
+                       script = "/usr/local/bin/gfortran -g -m64 -c ${PROJECT_DIR}/${INPUT_FILE_NAME} -o ${TARGET_BUILD_DIR}/${INPUT_FILE_BASE}.o";
                };
 /* End PBXBuildRule section */
 
                8DD76FAF0486AB0100D96B5E /* CopyFiles */ = {
                        isa = PBXCopyFilesBuildPhase;
                        buildActionMask = 8;
-                       dstPath = /usr/share/man/man1/;
-                       dstSubfolderSpec = 0;
+                       dstPath = Users/SarahsWork/desktop/debug;
+                       dstSubfolderSpec = 16;
                        files = (
                                8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */,
                        );
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
+               219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = newcommandtemplate.cpp; sourceTree = "<group>"; };
+               219C1DE11552C508004209F9 /* newcommandtemplate.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = newcommandtemplate.h; sourceTree = "<group>"; };
+               219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcoremicrobiomecommand.cpp; sourceTree = "<group>"; };
+               219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcoremicrobiomecommand.h; sourceTree = "<group>"; };
                7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
-               8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = regularizedrandomforest.cpp; sourceTree = "<group>"; };
+               834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = regularizedrandomforest.h; sourceTree = "<group>"; };
+               834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = regularizeddecisiontree.cpp; sourceTree = "<group>"; };
+               834D9D5B1656DEC700E7FAB9 /* regularizeddecisiontree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = regularizeddecisiontree.h; sourceTree = "<group>"; };
+               83F25B0A163B031200ABE73D /* forest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = forest.cpp; sourceTree = "<group>"; };
+               83F25B0B163B031200ABE73D /* forest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = forest.h; sourceTree = "<group>"; };
+               8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               A70056E5156A93D000924A2D /* getotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getotulabelscommand.cpp; sourceTree = "<group>"; };
+               A70056E8156A93E300924A2D /* getotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getotulabelscommand.h; sourceTree = "<group>"; };
+               A70056E9156AB6D400924A2D /* removeotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotulabelscommand.h; sourceTree = "<group>"; };
+               A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotulabelscommand.cpp; sourceTree = "<group>"; };
                A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+               A7128B1A16B7001200723BE4 /* getdistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getdistscommand.h; sourceTree = "<group>"; };
+               A7128B1C16B7002600723BE4 /* getdistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getdistscommand.cpp; sourceTree = "<group>"; };
                A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
                A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
                A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = "<group>"; };
                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergegroupscommand.cpp; sourceTree = "<group>"; };
                A721765513BB9F7D0014DAAE /* referencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = referencedb.h; sourceTree = "<group>"; };
                A721765613BB9F7D0014DAAE /* referencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = referencedb.cpp; sourceTree = "<group>"; };
+               A721AB66161C570F009860A1 /* alignnode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignnode.cpp; sourceTree = "<group>"; };
+               A721AB67161C570F009860A1 /* alignnode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignnode.h; sourceTree = "<group>"; };
+               A721AB68161C570F009860A1 /* aligntree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligntree.cpp; sourceTree = "<group>"; };
+               A721AB69161C570F009860A1 /* aligntree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = aligntree.h; sourceTree = "<group>"; };
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                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = "<group>"; };
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-               A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensusseqscommand.cpp; sourceTree = "<group>"; };
+               A7E9B6B512D37EC400DA6239 /* consensus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensus.cpp; sourceTree = "<group>"; };
+               A7E9B6B612D37EC400DA6239 /* consensus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensus.h; sourceTree = "<group>"; };
+               A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = consensusseqscommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensusseqscommand.h; sourceTree = "<group>"; };
                A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = corraxescommand.cpp; sourceTree = "<group>"; };
                A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = corraxescommand.h; sourceTree = "<group>"; };
                A7E9B6C212D37EC400DA6239 /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = "<group>"; };
                A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
                A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
-               A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = degapseqscommand.cpp; sourceTree = "<group>"; };
+               A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = degapseqscommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = degapseqscommand.h; sourceTree = "<group>"; };
                A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deuniqueseqscommand.cpp; sourceTree = "<group>"; };
                A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deuniqueseqscommand.h; sourceTree = "<group>"; };
                A7E9B6C912D37EC400DA6239 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = SOURCE_ROOT; };
                A7E9B6CA12D37EC400DA6239 /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = "<group>"; };
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+               A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = distancecommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B6CC12D37EC400DA6239 /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = "<group>"; };
                A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = "<group>"; };
                A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = "<group>"; };
                A7E9B6E212D37EC400DA6239 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = "<group>"; };
                A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = "<group>"; };
                A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = "<group>"; };
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                A7E9B6E712D37EC400DA6239 /* flowdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = flowdata.cpp; sourceTree = "<group>"; };
                A7E9B6E812D37EC400DA6239 /* flowdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = flowdata.h; sourceTree = "<group>"; };
                A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = "<group>"; };
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                A7E9B6F012D37EC400DA6239 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = "<group>"; };
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+               A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = getgroupcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
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                A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupscommand.cpp; sourceTree = "<group>"; };
                A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupscommand.h; sourceTree = "<group>"; };
                A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = "<group>"; };
                A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getotuscommand.cpp; sourceTree = "<group>"; };
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                A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = "<group>"; };
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+               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = makegroupcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
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                A7E9B74512D37EC400DA6239 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = "<group>"; };
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                A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = "<group>"; };
                A7E9B75412D37EC400DA6239 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = "<group>"; };
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                A7E9B7B312D37EC400DA6239 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = "<group>"; };
                A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = "<group>"; };
                A7E9B7B512D37EC400DA6239 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
-               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
-               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
                A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
-               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
-               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
                A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
                A7E9B7BE12D37EC400DA6239 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
                A7E9B7BF12D37EC400DA6239 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
                A7E9B7C012D37EC400DA6239 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
-               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
-               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = "<group>"; };
                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = "<group>"; };
                A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = "<group>"; };
                A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; };
                A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
                A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
+               A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifytreecommand.cpp; sourceTree = "<group>"; };
+               A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifytreecommand.h; sourceTree = "<group>"; };
                A7F9F5CD141A5E500032F693 /* sequenceparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequenceparser.h; sourceTree = "<group>"; };
                A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequenceparser.cpp; sourceTree = "<group>"; };
                A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = "<group>"; };
                                A7A61F1A130035C800E05B6B /* LICENSE */,
                                A70332B512D3A13400761E33 /* makefile */,
                                A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */,
+                               A77B718A173D40E4002163C2 /* calcsparcc.h */,
+                               A77B7189173D40E4002163C2 /* calcsparcc.cpp */,
                                A7E9BA4F12D398D700DA6239 /* clearcut */,
                                A7E9B69812D37EC400DA6239 /* cluster.cpp */,
                                A7E9B69912D37EC400DA6239 /* cluster.hpp */,
                                A7DAAFA3133A254E003956EB /* commandparameter.h */,
                                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
                                A7E9BA4212D3960D00DA6239 /* containers */,
+                               A7E9B6B612D37EC400DA6239 /* consensus.h */,
+                               A7E9B6B512D37EC400DA6239 /* consensus.cpp */,
                                A7AACFBA132FE008003D6C4D /* currentfile.h */,
                                A7E9B6C912D37EC400DA6239 /* display.h */,
                                A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */,
                                A7E9B77C12D37EC400DA6239 /* overlap.hpp */,
                                A7E9B79B12D37EC400DA6239 /* progress.cpp */,
                                A7E9B79C12D37EC400DA6239 /* progress.hpp */,
+                               A7548FAF171440ED00B1F05A /* qFinderDMM.h */,
+                               A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */,
+                               A77B7187173D4041002163C2 /* randomnumber.h */,
+                               A77B7186173D4041002163C2 /* randomnumber.cpp */,
                                A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */,
+                               A7386C191619C9FB00651424 /* randomforest */,
                                A7E9B7A612D37EC400DA6239 /* rarecalc.h */,
                                A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */,
                                A7E9B7A812D37EC400DA6239 /* raredisplay.h */,
                                A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
                                A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
                                A7E9B83112D37EC400DA6239 /* slibshuff.h */,
+                               A7876A28152A018B00A0AE86 /* subsample.h */,
+                               A7876A25152A017C00A0AE86 /* subsample.cpp */,
+                               A7C3DC0E14FE469500FE1924 /* trialswap2.h */,
+                               A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */,
                                A7FF19F0140FFDA500AD216D /* trimoligos.h */,
                                A7FF19F1140FFDA500AD216D /* trimoligos.cpp */,
                                A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76FB20486AB0100D96B5E /* Mothur */,
+                               8DD76FB20486AB0100D96B5E /* mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                };
-               A74D3644137DA7CE00332B0C /* uchime */ = {
+               A7386C191619C9FB00651424 /* randomforest */ = {
                        isa = PBXGroup;
                        children = (
-                               A74D3655137DAB8300332B0C /* addtargets2.cpp */,
-                               A74D3656137DAB8300332B0C /* alignchime.cpp */,
-                               A74D3657137DAB8300332B0C /* alignchimel.cpp */,
-                               A74D3658137DAB8300332B0C /* allocs.h */,
-                               A74D3659137DAB8300332B0C /* alnheuristics.h */,
-                               A74D365A137DAB8300332B0C /* alnparams.cpp */,
-                               A74D365B137DAB8300332B0C /* alnparams.h */,
-                               A74D365C137DAB8300332B0C /* alpha.cpp */,
-                               A74D365D137DAB8300332B0C /* alpha.h */,
-                               A74D365E137DAB8300332B0C /* alpha2.cpp */,
-                               A74D365F137DAB8300332B0C /* chainer.h */,
-                               A74D3660137DAB8300332B0C /* chime.h */,
-                               A74D3661137DAB8300332B0C /* diagbox.h */,
-                               A74D3662137DAB8300332B0C /* dp.h */,
-                               A74D3663137DAB8300332B0C /* evalue.h */,
-                               A74D3664137DAB8300332B0C /* fractid.cpp */,
-                               A74D3665137DAB8300332B0C /* getparents.cpp */,
-                               A74D3666137DAB8300332B0C /* globalalign2.cpp */,
-                               A74D3667137DAB8300332B0C /* help.h */,
-                               A74D3668137DAB8300332B0C /* hsp.h */,
-                               A74D3669137DAB8300332B0C /* hspfinder.h */,
-                               A74D366A137DAB8300332B0C /* make3way.cpp */,
-                               A74D366B137DAB8300332B0C /* mx.cpp */,
-                               A74D366C137DAB8300332B0C /* mx.h */,
-                               A74D366D137DAB8300332B0C /* myopts.h */,
-                               A74D366E137DAB8300332B0C /* myutils.cpp */,
-                               A74D366F137DAB8300332B0C /* myutils.h */,
-                               A74D3670137DAB8300332B0C /* orf.h */,
-                               A74D3671137DAB8300332B0C /* out.h */,
-                               A74D3672137DAB8300332B0C /* path.cpp */,
-                               A74D3673137DAB8300332B0C /* path.h */,
-                               A74D3674137DAB8300332B0C /* searchchime.cpp */,
-                               A74D3675137DAB8300332B0C /* seq.h */,
-                               A74D3676137DAB8300332B0C /* seqdb.cpp */,
-                               A74D3677137DAB8300332B0C /* seqdb.h */,
-                               A74D3678137DAB8300332B0C /* setnucmx.cpp */,
-                               A74D3679137DAB8300332B0C /* sfasta.cpp */,
-                               A74D367A137DAB8300332B0C /* sfasta.h */,
-                               A74D367B137DAB8300332B0C /* svnmods.h */,
-                               A74D367C137DAB8300332B0C /* svnversion.h */,
-                               A74D367D137DAB8300332B0C /* timers.h */,
-                               A74D367E137DAB8300332B0C /* timing.h */,
-                               A74D367F137DAB8300332B0C /* tracebackbit.cpp */,
-                               A74D3680137DAB8300332B0C /* uc.h */,
-                               A74D3681137DAB8300332B0C /* uchime_main.cpp */,
-                               A74D3682137DAB8300332B0C /* ultra.h */,
-                               A74D3683137DAB8300332B0C /* usort.cpp */,
-                               A74D3684137DAB8300332B0C /* viterbifast.cpp */,
-                               A74D3685137DAB8300332B0C /* windex.h */,
-                               A74D3686137DAB8300332B0C /* writechhit.cpp */,
+                               A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */,
+                               A7386C241619E52200651424 /* abstractdecisiontree.cpp */,
+                               A7386C1D1619CACB00651424 /* decisiontree.hpp */,
+                               A7386C28161A110700651424 /* decisiontree.cpp */,
+                               A7386C1E1619CACB00651424 /* macros.h */,
+                               A7386C1F1619CACB00651424 /* randomforest.hpp */,
+                               A77E1937161B201E00DB1A2A /* randomforest.cpp */,
+                               A7386C201619CACB00651424 /* rftreenode.hpp */,
+                               A77E193A161B289600DB1A2A /* rftreenode.cpp */,
+                               83F25B0A163B031200ABE73D /* forest.cpp */,
+                               83F25B0B163B031200ABE73D /* forest.h */,
+                               834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */,
+                               834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */,
+                               834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */,
+                               834D9D5B1656DEC700E7FAB9 /* regularizeddecisiontree.h */,
                        );
-                       name = uchime;
+                       name = randomforest;
                        sourceTree = "<group>";
                };
                A7D161E7149F7F50000523E8 /* fortran */ = {
                        isa = PBXGroup;
                        children = (
                                A7E9B6AE12D37EC400DA6239 /* command.hpp */,
+                               219C1DE11552C508004209F9 /* newcommandtemplate.h */,
+                               219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */,
                                A7E9B65212D37EC300DA6239 /* aligncommand.h */,
                                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
                                A7A61F2B130062E000E05B6B /* amovacommand.h */,
                                A71CB15E130B04A2001E7287 /* anosimcommand.cpp */,
                                A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
                                A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
-                               A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */,
-                               A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
                                A7E9B67312D37EC400DA6239 /* catchallcommand.h */,
                                A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
                                A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */,
                                A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */,
                                A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */,
                                A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
+                               A7386C221619CCE600651424 /* classifysharedcommand.h */,
+                               A7386C211619CCE600651424 /* classifysharedcommand.cpp */,
+                               A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */,
+                               A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */,
                                A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
                                A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */,
                                A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */,
                                A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */,
                                A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */,
                                A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */,
-                               A7E9B6B612D37EC400DA6239 /* consensuscommand.h */,
-                               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */,
                                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */,
                                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
+                               A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */,
+                               A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */,
                                A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
                                A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
                                A795840B13F13CD900F201D5 /* countgroupscommand.h */,
                                A795840C13F13CD900F201D5 /* countgroupscommand.cpp */,
                                A7730EFD13967241007433A3 /* countseqscommand.h */,
                                A7730EFE13967241007433A3 /* countseqscommand.cpp */,
+                               A77EBD2C1523707F00ED407C /* createdatabasecommand.h */,
+                               A77EBD2E1523709100ED407C /* createdatabasecommand.cpp */,
                                A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
                                A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
                                A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */,
                                A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
                                A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
                                A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
+                               A79EEF8816971D640006DEC1 /* filtersharedcommand.h */,
+                               A79EEF8516971D4A0006DEC1 /* filtersharedcommand.cpp */,
                                A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */,
                                A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */,
+                               219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */,
+                               219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */,
                                A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
                                A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
+                               A7128B1A16B7001200723BE4 /* getdistscommand.h */,
+                               A7128B1C16B7002600723BE4 /* getdistscommand.cpp */,
                                A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
                                A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
                                A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */,
                                A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
                                A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */,
                                A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
+                               A7548FAB17142EA500B1F05A /* getmetacommunitycommand.h */,
+                               A7548FAC17142EBC00B1F05A /* getmetacommunitycommand.cpp */,
+                               A70056E8156A93E300924A2D /* getotulabelscommand.h */,
+                               A70056E5156A93D000924A2D /* getotulabelscommand.cpp */,
                                A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */,
                                A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
                                A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */,
                                A75790581301749D00A30DAB /* homovacommand.cpp */,
                                A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */,
                                A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
+                               A7496D2D167B531B00CC7D7C /* kruskalwalliscommand.h */,
+                               A7496D2C167B531B00CC7D7C /* kruskalwalliscommand.cpp */,
                                A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
                                A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
+                               A7A0671C156294810095C8C5 /* listotulabelscommand.h */,
+                               A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */,
                                A7E9B73E12D37EC400DA6239 /* listseqscommand.h */,
                                A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
+                               A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */,
+                               A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */,
                                A7FA10001302E096003860FE /* mantelcommand.h */,
                                A7FA10011302E096003860FE /* mantelcommand.cpp */,
+                               A724D2B4153C8600000A826F /* makebiomcommand.h */,
+                               A724D2B6153C8628000A826F /* makebiomcommand.cpp */,
+                               A7A0671D1562AC230095C8C5 /* makecontigscommand.h */,
+                               A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */,
                                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */,
                                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */,
                                A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
                                A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */,
+                               A7E6F69C17427CF2006775E2 /* makelookupcommand.h */,
+                               A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */,
                                A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
                                A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
                                A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
                                A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
                                A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
                                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
+                               A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */,
+                               A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */,
                                A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
                                A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
                                A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */,
                                A7FC486612D795D60055BC5C /* pcacommand.cpp */,
                                A7E9B78812D37EC400DA6239 /* pcoacommand.h */,
                                A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
+                               A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */,
+                               A76CDD811510F143004C8458 /* prcseqscommand.cpp */,
                                A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */,
                                A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
                                A7E9B79212D37EC400DA6239 /* phylotypecommand.h */,
                                A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */,
                                A7E9B79812D37EC400DA6239 /* preclustercommand.h */,
                                A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */,
+                               A74C06E616A9C097008390A3 /* primerdesigncommand.h */,
+                               A74C06E816A9C0A8008390A3 /* primerdesigncommand.cpp */,
                                A7E9B7A212D37EC400DA6239 /* quitcommand.h */,
                                A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */,
                                A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */,
                                A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
                                A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
                                A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
-                               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */,
-                               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */,
-                               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */,
-                               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */,
-                               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */,
-                               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */,
+                               A7B0231716B8245D006BA09E /* removedistscommand.h */,
+                               A7B0231416B8244B006BA09E /* removedistscommand.cpp */,
                                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
                                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
                                A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
                                A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */,
                                A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
                                A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
+                               A70056E9156AB6D400924A2D /* removeotulabelscommand.h */,
+                               A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */,
                                A727864212E9E28C00F86ABA /* removerarecommand.h */,
                                A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
                                A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
                                A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
+                               A7CFA42F1755400500D9ED4D /* renameseqscommand.h */,
+                               A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */,
                                A7E9B7CE12D37EC400DA6239 /* reversecommand.h */,
                                A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
                                A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */,
                                A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
                                A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */,
                                A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
+                               A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */,
+                               A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */,
                                A7E9B7F312D37EC400DA6239 /* sharedcommand.h */,
                                A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
                                A774101314695AF60098E6AC /* shhhseqscommand.cpp */,
                                A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */,
                                A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */,
+                               A77B7183173D222F002163C2 /* sparcccommand.h */,
+                               A77B7184173D2240002163C2 /* sparcccommand.cpp */,
                                A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
                                A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
                                A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
                                A7E9B67112D37EC400DA6239 /* canberra.h */,
                                A7E9B67612D37EC400DA6239 /* chao1.cpp */,
                                A7E9B67712D37EC400DA6239 /* chao1.h */,
-                               A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
-                               A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
                                A7E9B6BB12D37EC400DA6239 /* coverage.cpp */,
                                A7E9B6BC12D37EC400DA6239 /* coverage.h */,
                                A7E9B6CA12D37EC400DA6239 /* dist.h */,
                                A7E9B66312D37EC400DA6239 /* blastalign.hpp */,
                                A7E9B66412D37EC400DA6239 /* blastdb.cpp */,
                                A7E9B66512D37EC400DA6239 /* blastdb.hpp */,
+                               A74D59A6159A1E3600043046 /* counttable.h */,
+                               A74D59A3159A1E2000043046 /* counttable.cpp */,
                                A7E9B6BD12D37EC400DA6239 /* database.cpp */,
                                A7E9B6BE12D37EC400DA6239 /* database.hpp */,
                                A7E9B6BF12D37EC400DA6239 /* datavector.hpp */,
-                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */,
+                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */,
                                A7E9B6DF12D37EC400DA6239 /* fastamap.h */,
                                A7E9B6E812D37EC400DA6239 /* flowdata.h */,
                                A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */,
                                A7E9B7DB12D37EC400DA6239 /* sequence.cpp */,
                                A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
+                               A741FAD415D168A00067BCC5 /* sequencecountparser.h */,
+                               A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */,
                                A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
                                A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
                                A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
                                A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
                                A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */,
+                               A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */,
                                A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
                                A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
                                A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
                A7E9BA4512D3965600DA6239 /* chimera */ = {
                        isa = PBXGroup;
                        children = (
-                               A74D3644137DA7CE00332B0C /* uchime */,
                                A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */,
                                A7E9B65D12D37EC300DA6239 /* bellerophon.h */,
                                A7E9B67412D37EC400DA6239 /* ccode.cpp */,
                A7E9BA4B12D3966900DA6239 /* classifier */ = {
                        isa = PBXGroup;
                        children = (
-                               A7E9B65A12D37EC300DA6239 /* bayesian.cpp */,
+                               A721AB67161C570F009860A1 /* alignnode.h */,
+                               A721AB66161C570F009860A1 /* alignnode.cpp */,
+                               A721AB69161C570F009860A1 /* aligntree.h */,
+                               A721AB68161C570F009860A1 /* aligntree.cpp */,
                                A7E9B65B12D37EC300DA6239 /* bayesian.h */,
+                               A7E9B65A12D37EC300DA6239 /* bayesian.cpp */,
                                A7E9B68E12D37EC400DA6239 /* classify.cpp */,
                                A7E9B68F12D37EC400DA6239 /* classify.h */,
+                               A721AB6E161C572A009860A1 /* kmernode.h */,
+                               A721AB6D161C572A009860A1 /* kmernode.cpp */,
+                               A721AB70161C572A009860A1 /* kmertree.h */,
+                               A721AB6F161C572A009860A1 /* kmertree.cpp */,
                                A7E9B73812D37EC400DA6239 /* knn.h */,
                                A7E9B73712D37EC400DA6239 /* knn.cpp */,
-                               A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */,
-                               A7E9B78A12D37EC400DA6239 /* phylodiversity.h */,
                                A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */,
                                A7E9B78E12D37EC400DA6239 /* phylosummary.h */,
                                A7E9B78F12D37EC400DA6239 /* phylotree.cpp */,
                                A7E9B79012D37EC400DA6239 /* phylotree.h */,
                                A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */,
                                A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */,
+                               A721AB74161C573B009860A1 /* taxonomynode.h */,
+                               A721AB73161C573B009860A1 /* taxonomynode.cpp */,
                        );
                        name = classifier;
                        sourceTree = "<group>";
                        children = (
                                A7E9B69412D37EC400DA6239 /* clearcut.cpp */,
                                A7E9B69512D37EC400DA6239 /* clearcut.h */,
+                               A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
+                               A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
                                A7E9B6B312D37EC400DA6239 /* common.h */,
                                A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */,
                                A7E9B6D012D37EC400DA6239 /* distclearcut.h */,
                                A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
                                A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
                                A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
+                               A7D755D71535F665009BF21A /* treereader.h */,
+                               A7D755D91535F679009BF21A /* treereader.cpp */,
                        );
                        name = read;
                        sourceTree = "<group>";
                        isa = PBXGroup;
                        children = (
                                A7D161E7149F7F50000523E8 /* fortran */,
-                               A7E9B6E512D37EC400DA6239 /* fisher2.c */,
-                               A7E9B6E612D37EC400DA6239 /* fisher2.h */,
-                               A7E9B75512D37EC400DA6239 /* metastats.h */,
-                               A7E9B75612D37EC400DA6239 /* metastats2.c */,
                                A79234D513C74BF6002B08E2 /* mothurfisher.h */,
                                A79234D613C74BF6002B08E2 /* mothurfisher.cpp */,
                                A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */,
                        name = Mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = mothur;
-                       productReference = 8DD76FB20486AB0100D96B5E /* Mothur */;
+                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
                        attributes = {
+                               LastUpgradeCheck = 0460;
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
                        buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
-                       compatibilityVersion = "Xcode 3.1";
+                       compatibilityVersion = "Xcode 3.2";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
                        knownRegions = (
                                A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */,
                                A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */,
                                A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */,
-                               A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */,
                                A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */,
                                A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */,
                                A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */,
                                A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */,
                                A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */,
                                A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */,
-                               A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */,
+                               A7E9B8B312D37EC400DA6239 /* consensus.cpp in Sources */,
                                A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */,
                                A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */,
                                A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */,
                                A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */,
                                A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */,
                                A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */,
-                               A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */,
                                A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */,
                                A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */,
                                A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */,
                                A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */,
                                A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */,
                                A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */,
-                               A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */,
                                A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */,
                                A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */,
                                A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */,
                                A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */,
                                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
                                A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */,
-                               A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */,
                                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */,
                                A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */,
                                A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */,
                                A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */,
                                A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */,
                                A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */,
-                               A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */,
-                               A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */,
                                A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */,
                                A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */,
-                               A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */,
                                A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */,
                                A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */,
                                A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */,
                                A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */,
                                A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */,
                                A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */,
-                               A74D3687137DAB8300332B0C /* addtargets2.cpp in Sources */,
-                               A74D3688137DAB8400332B0C /* alignchime.cpp in Sources */,
-                               A74D3689137DAB8400332B0C /* alignchimel.cpp in Sources */,
-                               A74D368A137DAB8400332B0C /* alnparams.cpp in Sources */,
-                               A74D368B137DAB8400332B0C /* alpha.cpp in Sources */,
-                               A74D368C137DAB8400332B0C /* alpha2.cpp in Sources */,
-                               A74D368D137DAB8400332B0C /* fractid.cpp in Sources */,
-                               A74D368E137DAB8400332B0C /* getparents.cpp in Sources */,
-                               A74D368F137DAB8400332B0C /* globalalign2.cpp in Sources */,
-                               A74D3690137DAB8400332B0C /* make3way.cpp in Sources */,
-                               A74D3691137DAB8400332B0C /* mx.cpp in Sources */,
-                               A74D3692137DAB8400332B0C /* myutils.cpp in Sources */,
-                               A74D3693137DAB8400332B0C /* path.cpp in Sources */,
-                               A74D3694137DAB8400332B0C /* searchchime.cpp in Sources */,
-                               A74D3695137DAB8400332B0C /* seqdb.cpp in Sources */,
-                               A74D3696137DAB8400332B0C /* setnucmx.cpp in Sources */,
-                               A74D3697137DAB8400332B0C /* sfasta.cpp in Sources */,
-                               A74D3698137DAB8400332B0C /* tracebackbit.cpp in Sources */,
-                               A74D3699137DAB8400332B0C /* uchime_main.cpp in Sources */,
-                               A74D369A137DAB8400332B0C /* usort.cpp in Sources */,
-                               A74D369B137DAB8400332B0C /* viterbifast.cpp in Sources */,
-                               A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */,
                                A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */,
                                A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */,
                                A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */,
                                A7FA2B5B14A0F0C2007C09A6 /* intrv.f in Sources */,
                                A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */,
                                A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */,
+                               A7EEB0F514F29BFE00344B83 /* classifytreecommand.cpp in Sources */,
+                               A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */,
+                               A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */,
+                               A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */,
+                               A77EBD2F1523709100ED407C /* createdatabasecommand.cpp in Sources */,
+                               A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */,
+                               A7D755DA1535F679009BF21A /* treereader.cpp in Sources */,
+                               A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */,
+                               219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */,
+                               219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */,
+                               A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */,
+                               A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */,
+                               A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */,
+                               A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */,
+                               A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */,
+                               A74D59A4159A1E2000043046 /* counttable.cpp in Sources */,
+                               A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */,
+                               A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */,
+                               A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */,
+                               A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */,
+                               A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */,
+                               A7386C29161A110800651424 /* decisiontree.cpp in Sources */,
+                               A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */,
+                               A77E193B161B289600DB1A2A /* rftreenode.cpp in Sources */,
+                               A721AB6A161C570F009860A1 /* alignnode.cpp in Sources */,
+                               A721AB6B161C570F009860A1 /* aligntree.cpp in Sources */,
+                               A721AB71161C572A009860A1 /* kmernode.cpp in Sources */,
+                               A721AB72161C572A009860A1 /* kmertree.cpp in Sources */,
+                               A721AB77161C573B009860A1 /* taxonomynode.cpp in Sources */,
+                               83F25B0C163B031200ABE73D /* forest.cpp in Sources */,
+                               834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */,
+                               834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */,
+                               A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */,
+                               A79EEF8616971D4A0006DEC1 /* filtersharedcommand.cpp in Sources */,
+                               A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */,
+                               A7128B1D16B7002A00723BE4 /* getdistscommand.cpp in Sources */,
+                               A7B0231516B8244C006BA09E /* removedistscommand.cpp in Sources */,
+                               A799314B16CBD0CD0017E888 /* mergetaxsummarycommand.cpp in Sources */,
+                               A7548FAD17142EBC00B1F05A /* getmetacommunitycommand.cpp in Sources */,
+                               A7548FB0171440ED00B1F05A /* qFinderDMM.cpp in Sources */,
+                               A77B7185173D2240002163C2 /* sparcccommand.cpp in Sources */,
+                               A77B7188173D4042002163C2 /* randomnumber.cpp in Sources */,
+                               A77B718B173D40E5002163C2 /* calcsparcc.cpp in Sources */,
+                               A7E6F69E17427D06006775E2 /* makelookupcommand.cpp in Sources */,
+                               A7CFA4311755401800D9ED4D /* renameseqscommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                        buildSettings = {
                                ALWAYS_SEARCH_USER_PATHS = NO;
                                COPY_PHASE_STRIP = NO;
+                               DEPLOYMENT_LOCATION = YES;
+                               DSTROOT = TARGET_BUILD_DIR;
+                               "DSTROOT[sdk=*]" = TARGET_BUILD_DIR;
                                GCC_DYNAMIC_NO_PIC = NO;
-                               GCC_ENABLE_FIX_AND_CONTINUE = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 3;
-                               INSTALL_PATH = /usr/local/bin;
-                               PRODUCT_NAME = Mothur;
-                               SDKROOT = macosx10.6;
+                               "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
+                               PRODUCT_NAME = mothur;
+                               SDKROOT = macosx10.8;
+                               SKIP_INSTALL = NO;
                        };
                        name = Debug;
                };
                                ALWAYS_SEARCH_USER_PATHS = NO;
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                DEPLOYMENT_LOCATION = YES;
+                               DSTROOT = TARGET_BUILD_DIR;
                                GCC_MODEL_TUNING = G5;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_UNUSED_VALUE = YES;
-                               INSTALL_PATH = ./;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
+                               SDKROOT = macosx;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };
                                GCC_ENABLE_SSE3_EXTENSIONS = NO;
                                GCC_ENABLE_SSE41_EXTENSIONS = NO;
                                GCC_ENABLE_SSE42_EXTENSIONS = NO;
-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = s;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.23.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"1/9/2012\\\"\"",
+                                       "MOTHUR_FILES=\"\\\"../../release\\\"\"",
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
                                "GCC_VERSION[arch=*]" = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                HEADER_SEARCH_PATHS = "";
-                               INSTALL_PATH = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               PREBINDING = NO;
-                               SDKROOT = macosx10.6;
+                               SDKROOT = macosx;
+                               SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
                        name = Debug;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
                                GCC_MODEL_TUNING = "";
-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = s;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "VERSION=\"\\\"1.19.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"5/9/2011\\\"\"",
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_PARAMETER = YES;
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               INSTALL_PATH = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-DUSE_READLINE",
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               PREBINDING = NO;
-                               SDKROOT = macosx10.6;
+                               SDKROOT = macosx;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };
                                1DEB928708733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
-                       defaultConfigurationName = Release;
+                       defaultConfigurationName = Debug;
                };
                1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                                1DEB928B08733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
-                       defaultConfigurationName = Release;
+                       defaultConfigurationName = Debug;
                };
 /* End XCConfigurationList section */
        };